Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Samples for metagenomic sequencing were collected from the Eastern Tropical North Pacific (ETNP) Oxygen Minimum Zone (OMZ) on R/V Sally Ride (SR2114) from December 2021 to January 2022. Sea water for metagenomes was collected from all nine depths for all five sampling stations. Collections were made using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus), as described in Tsementzi et al., 2016.

DNA was extracted from biomass on collecting filters using the MoBio Power Soil kit (MoBio Inc. Carlsbad, CA, USA) and libraries were prepared for metagenomic sequencing using the Illumina DNA library prep kit with unique dual indexing according to manufacturer's instructions, except that the protocol was terminated after isolation of cleaned double stranded libraries. An equimolar mixture of the libraries was 2 sequenced on an Illumina NovaSeq 6000 instrument at the Molecular Evolution Core, Georgia Institute of Technology.

The raw shotgun metagenomes are provided, and are available in NCBI under BioProject number PRJNA1124864.

- Imported original Excel file "Table S2. Sample information for the metagenomes from the ETNP OMZ.xlsx" (sheet 1) into the BCO-DMO data processing system.
- Converted "Date Sampled" from format "%m-%d-%y" to "%Y-%m-%d".
- Converted "Date Extracted" from format "%m.%d.%y" to "%Y-%m-%d".
- Converted "Lat N" from degrees-decimal_minutes format to decimal degrees using directional N, and renamed the new column "Latitude".
- Converted "Long W" from degrees-decimal_minutes format to decimal degrees using directional W, and renamed the new column "Longitude".
- Rounded Latitude and Longitude to maximum 4 decimal places.
- Renamed columns to comply with BCO-DMO naming conventions.
- Saved the final file as "998771_v1_etnp_metagenomes_zhao.csv".

NSF Award Abstract:
This project studies how low oxygen availability influences the biodiversity and ecological role of SAR11 bacteria, one of the most abundant microbial groups in the ocean. The work involves oceanographic sampling across a range of oxygen and nutrient levels in the Eastern Tropical North Pacific Ocean. Using a combination of genomic, microbiological, and biogeochemical methods, the study identifies the mechanisms by which SAR11 strains diversify into separate niches and species and contribute biochemically to the ecosystem, likely through removing nitrogen from seawater. The project equips the next generation of researchers and educators, notably those from underrepresented minority groups, to use oceanographic, genomic, and microbiological concepts to meet contemporary scientific challenges. This goal is met through a combination of bioinformatic workshops that target undergraduate students from the University System of Puerto Rico, middle school teacher-training workshops, and middle or high school teacher internships in the investigator’s labs. This multifaceted research and educational agenda fills a gap in our understanding of marine biological diversity, identifies the contribution of SAR11 bacteria to nutrient and carbon cycles in low oxygen oceans, and provides lessons and analytical tools to study microbial processes in other ecosystems.

This project has two aims. Aim 1 employs comparative metagenomic and single-cell genomic analyses to identify metabolic properties that distinguish SAR11 clades from low oxygen regions and processes of selection or gene flow operating across the clades. Aim 2 combines microbial transcriptomics, incubation experiments with isotope tracers, and culturing to delimit the oxygen and nutrient conditions that define the niche space of each SAR11 clade and to correlate SAR11 gene transcription with community biochemical outcomes, including nitrogen loss through denitrification. The results of these aims and the informatic methods used to probe microbial microdiversity are disseminated through genomics-focused undergraduate workshops, and new teacher-training educational modules, including lab-based modules focused on the importance of microorganisms under environmental change in the oceans. Data, manuscripts, and informatics workflows from this project are made publicly available. The results are critical for resolving the processes that create and sustain microbial diversity in the oceans and informing biogeochemical models that predict how diversity influences ecosystem processes.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.